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- PDB-6jwb: Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jwb | |||||||||
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Title | Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose | |||||||||
![]() | Endo-1,4-beta-xylanase 2![]() | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, C. / Wan, Q. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography. Authors: Li, Z. / Zhang, X. / Li, C. / Kovalevsky, A. / Wan, Q. #1: ![]() Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Authors: Wan, Q. #2: ![]() Year: 2014 Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism Authors: Jerry, M.P. / Wan, Q. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.9 KB | Display | ![]() |
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PDB format | ![]() | 103 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jugC ![]() 6k9oC ![]() 6k9rC ![]() 6k9wC ![]() 6kw9C ![]() 6kwcC ![]() 6kwdC ![]() 6kwfC ![]() 6kwgC ![]() 2dfcS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 20727.338 Da / Num. of mol.: 1 / Fragment: UNP residues 35-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose | ||
#3: Chemical | ChemComp-MES / ![]() | ||
#4: Chemical | ChemComp-IOD / ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow![]() | Temperature: 291 K / Method: evaporation / pH: 6 / Details: 20%PEG 8000, 0.2M NaI,0.1M MES |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.15→19.917 Å / Num. obs: 72399 / % possible obs: 99.86 % / Redundancy: 6 % / Biso Wilson estimate: 11.51 Å2 / Net I/σ(I): 18.41 |
Reflection shell | Resolution: 1.15→1.191 Å / Num. unique obs: 7143 / % possible all: 99.9 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 2DFC Resolution: 1.15→19.917 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.62 Å2 / Biso mean: 17.3456 Å2 / Biso min: 7.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→19.917 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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